public static void makeBonds(
ArrayList<Atom> atomList, ArrayList<Bond> bondList, int aLoc, int bLoc) {
Atom a = atomList.get(aLoc);
Atom b = atomList.get(bLoc);
if (aLoc != bLoc) {
// rough distance
if (getRoughDist(a, b) < maxBondLength) {
Double dist = getDist(a, b);
if (dist < maxBondLength) {
boolean skip = false;
// System.out.println(atomList.get(target).connectedTo.size());
for (int i = 0; i < b.connectedTo.size(); i++) {
if (b.connectedTo.get(i) == aLoc) {
skip = true;
}
}
if (!skip) {
Bond newBond = new Bond();
newBond.setTargets(aLoc, bLoc);
newBond.getBondAvg(a, b);
if (stick && dist <= newBond.getMaxDist()) {
newBond.setStick(true);
} else {
newBond.setStick(false);
}
bondList.add(newBond);
bondsMade++;
b.connectedTo.add(aLoc);
a.connectedTo.add(bLoc);
}
}
}
}
bondsChecked++;
}
